Molecular metrics status: done
Cached molecular metrics are available for this pose.
Metrics cached · SASA missing
py3Dmol interaction viewer
Left: interactive complex viewer. Right: clickable PLIP-like interaction summary. Clicking an interaction thickens and highlights it in the 3D view.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.814 kcal/mol/HA)
✓ Good fit quality (FQ -7.59)
✓ Good H-bonds (4 bonds)
✗ High strain energy (18.9 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-21.979
kcal/mol
LE
-0.814
kcal/mol/HA
Fit Quality
-7.59
FQ (Leeson)
HAC
27
heavy atoms
MW
387
Da
LogP
3.51
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, protein contact clashes, strain 18.9 kcal/mol
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 24
π–π 5
Clashes 11
Severe clashes 0
| Final rank | 5.0017875109194385 | Score | -21.9792 |
|---|---|---|---|
| Inter norm | -0.87165 | Intra norm | 0.0576055 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 4 |
| Artifact reason | geometry warning; 9 clashes; 11 protein contact clashes; high strain Δ 20.2 | ||
| Residues | A:ASN127;A:ASP161;A:CYS168;A:LEU208;A:LEU209;A:LYS178;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:PRO99;A:SER207;A:SER95;A:TRP221;A:TYR174;A:VAL206 | ||
Protein summary
275 residues
| Protein target | T07 | Atoms | 3932 |
|---|---|---|---|
| Residues | 275 | Chains | 3 |
| Residue summary | LEU:437; VAL:433; ALA:361; ARG:288; ILE:266; GLU:210; LYS:198; SER:198; ASN:182; THR:154; GLN:153; PHE:140; PRO:140; TYR:126; GLY:112; HIS:103 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | TbPTR1_cW_6RX6_Ready | Contacts | 19 |
|---|---|---|---|
| Pose | Open native pose | H-bonds | 6 |
| IFP residues | A:ARG14; A:ASP161; A:CYS168; A:GLY205; A:LEU208; A:LEU209; A:LYS178; A:MET213; A:NAP301; A:PHE171; A:PHE97; A:PRO210; A:PRO99; A:SER207; A:SER95; A:TRP221; A:TYR174; A:TYR98; A:VAL206 | ||
| Current overlap | 16 | Native recall | 0.84 |
| Jaccard | 0.80 | RMSD | - |
| H-bond strict | 2 | Strict recall | 0.33 |
| H-bond same residue+role | 3 | Role recall | 0.60 |
| H-bond same residue | 3 | Residue recall | 0.60 |
Hydrogen bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
Hydrophobic contacts
Clashes
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | Contacts | Native overlap | Native recall | HB role recall | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 295 | 2.6248326995720337 | -1.04839 | -25.698 | 3 | 15 | 14 | 0.74 | 0.20 | - | no | Open |
| 419 | 3.895463271160683 | -0.966028 | -22.426 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 323 | 4.565915127752357 | -0.856296 | -18.6325 | 2 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 322 | 4.6996822258351765 | -0.749027 | -18.7433 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 93 | 4.750220329559591 | -1.01697 | -20.9972 | 3 | 16 | 16 | 0.84 | 0.20 | - | no | Open |
| 319 | 4.787722288785993 | -0.860322 | -19.3331 | 2 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 310 | 5.0017875109194385 | -0.87165 | -21.9792 | 4 | 17 | 16 | 0.84 | 0.60 | - | no | Current |
| 491 | 5.092797929141489 | -0.869886 | -18.9182 | 2 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 87 | 5.431987139034222 | -0.775495 | -18.406 | 1 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 106 | 5.495972486877 | -0.809824 | -21.3114 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 490 | 5.5687415736876105 | -0.776667 | -17.7845 | 5 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 454 | 5.606773355888093 | -0.646318 | -15.8114 | 7 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 318 | 54.75142313912754 | -0.773082 | -18.2762 | 1 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 453 | 6.415587053861709 | -0.964684 | -25.8709 | 8 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 88 | 54.780493194146516 | -0.868266 | -19.382 | 2 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-21.979kcal/mol
Ligand efficiency (LE)
-0.8140kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.595
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
387.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.51
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.87kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
62.80kcal/mol
Minimised FF energy
43.92kcal/mol
SASA & burial (FreeSASA)
not yet run
SASA has not been computed yet for this pose. Queue a background recompute to populate FreeSASA burial metrics without blocking the page.